python bioinformagicks

python bioinformagicks#

A collection (read: hodgepodge) of tools for bioinformatics tasks.

Features#

Tools:

  • TF-IDF marker gene testing (“quickMarkers”), as in SoupX

  • JASMINE gene set scoring, as in Noureen et al.

  • Over-representation analyses (ORAs) with gProfiler

  • Cell mask generation based on geometric sketching, as in Geosketch

  • Cell mask generation based on embedding (i.e. UMAP) coordinate bounds

  • Z-standard scaling of gene expression on a per-group basis

  • Basic single-cell variant calling for single point mutations

Plotting:

  • Split embedding plot generation based on categorical observations

  • Stacked barplot generation of cell proportions split by group and counts normalized per-batch

  • Barplot generation for gProfiler ORA results, with optional term fold enrichment sorting

Utilities:

  • Identification of genes often left ignored, like AW146154

  • Combination of categorical columns maintaining specified ordering

Installation#

$ pip install python-bioinformagicks

Documentation#

https://python-bioinformagicks.readthedocs.io

Credits#

This package was created by Sylvia N. Michki.

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

License#

Free software: GNU General Public License v3

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